Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A5 F17 I0 R2	162	60.6	4616657	98.5%	4547407	62.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	1,303,631	C→T	100%	Q246Y (CAG→TAT)	oppA →	oligopeptide transporter subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,303,631	0	C	T	100.0%	196.9 / NA	65	Q246Y (CAG→TAT)	oppA	oligopeptide transporter subunit
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (37/28); total (37/28)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AACGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACCAGGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGAAAT  >  W3110S.gb/1303568‑1303695

aacgaacgAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAAc                                                           >  1:267217/1‑71 (MQ=255)

 acgaacgaATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAAcc                                                          >  1:3016121/1‑71 (MQ=255)

 acgaacgaATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAAcc                                                          >  1:2027347/1‑71 (MQ=255)

   gaacgaaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTa                                                        <  1:286724/71‑1 (MQ=255)

     acgaaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAtt                                                      >  1:1680898/1‑71 (MQ=255)

     acgaaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAtt                                                      <  1:2333385/71‑1 (MQ=255)

       gaaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAttt                                                     <  1:148863/70‑1 (MQ=255)

         aTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                                  >  1:281804/1‑71 (MQ=255)

          tCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAttt                                                     <  1:4518718/67‑1 (MQ=255)

           cGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCTAAAACCGTTATTAACTATGTAACCTATTTGCCTa                                                >  1:2095544/1‑71 (MQ=255)

           cGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTaa                                                            <  1:3391765/59‑1 (MQ=255)

           cGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAttt                                                     <  1:3030878/66‑1 (MQ=255)

            gTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTAt                                               >  1:104152/1‑71 (MQ=255)

              tCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTg                                             >  1:2857968/1‑71 (MQ=255)

               cTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGc                                            >  1:3505350/1‑71 (MQ=255)

                ttGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTg                                             >  1:67333/1‑69 (MQ=255)

                 tGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTa                                                        <  1:95693/57‑1 (MQ=255)

                  gAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTc                                         >  1:3856587/1‑71 (MQ=255)

                  gAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTc                                         >  1:2065140/1‑71 (MQ=255)

                  gAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTc                                         >  1:923491/1‑71 (MQ=255)

                   aaCGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTc                                         <  1:1841296/70‑1 (MQ=255)

                   aaCGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCt                                        <  1:703471/71‑1 (MQ=255)

                   aaCGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCt                                        <  1:1860911/71‑1 (MQ=255)

                    aCGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTg                                       <  1:2668707/71‑1 (MQ=255)

                     cGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGa                                      <  1:3913152/71‑1 (MQ=255)

                     cGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGa                                      <  1:1985816/71‑1 (MQ=255)

                      gCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTg                                       >  1:860012/1‑69 (MQ=255)

                      gCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGaa                                     <  1:1920564/71‑1 (MQ=255)

                        aGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAttt                                                     <  1:1671935/53‑1 (MQ=255)

                          cccGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAAc                                                           >  1:1718314/1‑45 (MQ=38)

                          cccGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCt                                                 <  1:988434/55‑1 (MQ=255)

                            cGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc                               >  1:565869/1‑71 (MQ=255)

                              aCCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGa                                      >  1:1069999/1‑62 (MQ=255)

                               ccTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGAt                            <  1:428125/71‑1 (MQ=255)

                               ccTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACATATTTGCCTATTGCTTCTGAAGTTAc                                >  1:3803156/1‑67 (MQ=255)

                                 tACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCtt                                          <  1:3361755/55‑1 (MQ=255)

                                  aCTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTa                                                <  1:2073170/48‑1 (MQ=39)

                                  aCTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGt                          >  1:4420637/1‑70 (MQ=255)

                                   cTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGt                                   >  1:1686993/1‑60 (MQ=255)

                                   cTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTc                         >  1:1928374/1‑70 (MQ=255)

                                    tGGAACAACGCGAAAACCGTTATTAACTATGTAAc                                                           >  1:339541/1‑35 (MQ=37)

                                    tGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGaa                                     >  1:3909872/1‑57 (MQ=255)

                                      gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCa                        >  1:2676618/1‑68 (MQ=255)

                                      gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCa                        >  1:2038400/1‑68 (MQ=255)

                                       aacaacGCGAAAACCGTTATTAACTATGTAACCTAt                                                       <  1:669851/36‑1 (MQ=37)

                                        acaacGCGAAAACCGTTATTAACTATGTAACCTAttt                                                     >  1:382108/1‑37 (MQ=37)

                                           acGCGAAAACCGTTATTAACTATGTAACCTATTTGc                                                   <  1:403092/36‑1 (MQ=37)

                                            cgcgAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCtt                                          >  1:198735/1‑44 (MQ=38)

                                             gcgAAAACCGTTATTAACTATGTAACCTATTTGCCt                                                 >  1:3279192/1‑36 (MQ=37)

                                             gcgAAAACCGTTATTAACTATGTAACCTATTTGCCTATAGCTTc                                         >  1:2670812/1‑44 (MQ=37)

                                              cgAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCg                              <  1:1846318/54‑1 (MQ=255)

                                              cgAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCg              >  1:929626/1‑70 (MQ=255)

                                              cgAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGt             <  1:4420616/71‑1 (MQ=255)

                                               gAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTa            <  1:1874817/71‑1 (MQ=255)

                                                aaaaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGAt                            >  1:2502684/1‑54 (MQ=255)

                                                aaaaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAg           <  1:2926871/71‑1 (MQ=255)

                                                 aaaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAgt          >  1:4575722/1‑71 (MQ=255)

                                                 aaaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAgt          >  1:1451853/1‑71 (MQ=255)

                                                  aaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAgtg         <  1:2240326/71‑1 (MQ=255)

                                                  aaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAgtg         <  1:695263/71‑1 (MQ=255)

                                                  aaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAgtg         >  1:2164572/1‑71 (MQ=255)

                                                      gTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAgtggtg      >  1:4389396/1‑70 (MQ=255)

                                                         attaACTATGTAACCTATTTGCCTATTGCTTCTGAAg                                    >  1:2035849/1‑37 (MQ=37)

                                                         attaACTATGTAACCTATTTGCCTATTGCTTCTGAAg                                    >  1:352221/1‑37 (MQ=37)

                                                          ttaACTATGTATCCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGAAAt  <  1:832251/70‑1 (MQ=255)

AACGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACCAGGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGAAAT  >  W3110S.gb/1303568‑1303695

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A